From c2e040272c497b1861b7e7f1af4dae9485ed4674 Mon Sep 17 00:00:00 2001 From: C-Achard Date: Fri, 3 May 2024 12:24:25 +0200 Subject: [PATCH 1/4] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 889b545f..6da8a1f4 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,7 @@ Then go into Plugins > napari-cellseg3d, and choose which tool to use. - **Review (label)**: This module allows you to review your labels, from predictions or manual labeling, and correct them if needed. It then saves the status of each file in a csv, for easier monitoring. - **Inference**: This module allows you to use pre-trained segmentation algorithms on volumes to automatically label cells and compute statistics. - **Train**: This module allows you to train segmentation algorithms from labeled volumes. -- **Utilities**: This module allows you to perform several actions like cropping your volumes and labels dynamically, by selecting a fixed size volume and moving it around the image; computing prediction scores from ground truth and predicition labels; or converting labels from instance to segmentation and the opposite. +- **Utilities**: This module allows you to perform several actions like cropping your volumes and labels dynamically, by selecting a fixed size volume and moving it around the image; fragment images into smaller cubes for training; or converting labels from instance to segmentation and the opposite. ## News From 11dba386575bff63cbc4a816d708da0a964dcf2d Mon Sep 17 00:00:00 2001 From: C-Achard Date: Fri, 3 May 2024 12:05:11 +0200 Subject: [PATCH 2/4] Update README for v0.1.3 --- README.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 6da8a1f4..adf2e59a 100644 --- a/README.md +++ b/README.md @@ -39,12 +39,15 @@ Then go into Plugins > napari-cellseg3d, and choose which tool to use. ## News -**New version : v0.1.2** +**New version : v0.1.3** -- Fixed manifest issue for PyPi +- Small API changes for training/inference from a script +- Changed project name to "napari_cellseg3d" to avoid setuptools deprecation +- Some fixes to WandB integration ad csv saving after training Previous additions : +- v0.1.2 :Fixed manifest issue for PyPi - Improved training interface - Unsupervised model : WNet3D - Generate labels directly from raw data! From 549cbf4643adcd252c6df67bdc0f687d1856dae8 Mon Sep 17 00:00:00 2001 From: C-Achard Date: Fri, 3 May 2024 12:25:41 +0200 Subject: [PATCH 3/4] Version bump --- napari_cellseg3d/__init__.py | 2 +- napari_cellseg3d/code_plugins/plugin_helper.py | 2 +- setup.cfg | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/napari_cellseg3d/__init__.py b/napari_cellseg3d/__init__.py index 9b7444d7..91489493 100644 --- a/napari_cellseg3d/__init__.py +++ b/napari_cellseg3d/__init__.py @@ -1,2 +1,2 @@ """napari-cellseg3d - napari plugin for cell segmentation.""" -__version__ = "0.1.2" +__version__ = "0.1.3" diff --git a/napari_cellseg3d/code_plugins/plugin_helper.py b/napari_cellseg3d/code_plugins/plugin_helper.py index 710d6ded..c5eba3dd 100644 --- a/napari_cellseg3d/code_plugins/plugin_helper.py +++ b/napari_cellseg3d/code_plugins/plugin_helper.py @@ -43,7 +43,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"): self.logo_label.setToolTip("Open Github page") self.info_label = ui.make_label( - f"You are using napari-cellseg3d v.{'0.1.2'}\n\n" + f"You are using napari-cellseg3d v.{'0.1.3'}\n\n" f"Plugin for cell segmentation developed\n" f"by the Mathis Lab of Adaptive Motor Control\n\n" f"Code by :\nCyril Achard\nMaxime Vidal\nJessy Lauer\nMackenzie Mathis\n" diff --git a/setup.cfg b/setup.cfg index a7fe8b0e..942b00c7 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = napari_cellseg3d -version = 0.1.2 +version = 0.1.3 [options] packages = find: From 9b35dedf6f1487edfa617e8a188bf38885efcc61 Mon Sep 17 00:00:00 2001 From: C-Achard Date: Fri, 3 May 2024 12:58:34 +0200 Subject: [PATCH 4/4] Version bump : 0.2.0 --- README.md | 4 ++-- napari_cellseg3d/__init__.py | 2 +- napari_cellseg3d/code_plugins/plugin_helper.py | 2 +- setup.cfg | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index adf2e59a..80e75b82 100644 --- a/README.md +++ b/README.md @@ -39,10 +39,10 @@ Then go into Plugins > napari-cellseg3d, and choose which tool to use. ## News -**New version : v0.1.3** +**New version : v0.2.0** -- Small API changes for training/inference from a script - Changed project name to "napari_cellseg3d" to avoid setuptools deprecation +- Small API changes for training/inference from a script - Some fixes to WandB integration ad csv saving after training Previous additions : diff --git a/napari_cellseg3d/__init__.py b/napari_cellseg3d/__init__.py index 91489493..e3d41f7a 100644 --- a/napari_cellseg3d/__init__.py +++ b/napari_cellseg3d/__init__.py @@ -1,2 +1,2 @@ """napari-cellseg3d - napari plugin for cell segmentation.""" -__version__ = "0.1.3" +__version__ = "0.2.0" diff --git a/napari_cellseg3d/code_plugins/plugin_helper.py b/napari_cellseg3d/code_plugins/plugin_helper.py index c5eba3dd..8a28d6cd 100644 --- a/napari_cellseg3d/code_plugins/plugin_helper.py +++ b/napari_cellseg3d/code_plugins/plugin_helper.py @@ -43,7 +43,7 @@ def __init__(self, viewer: "napari.viewer.Viewer"): self.logo_label.setToolTip("Open Github page") self.info_label = ui.make_label( - f"You are using napari-cellseg3d v.{'0.1.3'}\n\n" + f"You are using napari-cellseg3d v.{'0.2.0'}\n\n" f"Plugin for cell segmentation developed\n" f"by the Mathis Lab of Adaptive Motor Control\n\n" f"Code by :\nCyril Achard\nMaxime Vidal\nJessy Lauer\nMackenzie Mathis\n" diff --git a/setup.cfg b/setup.cfg index 942b00c7..9c36de55 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = napari_cellseg3d -version = 0.1.3 +version = 0.2.0 [options] packages = find: